My first attempt at a design gave a 52.6% confidence. When I clicked the "show neural net" option in the objectives, all 120 residues turn an identical shade of dark grey. Not one bit of red.
My design is awful. Why is the game telling me there is nothing to change?
That is a little odd if everything is exactly the same shade, and may indicate a bug. Can you share this solution with scientists?
But there could be other cases where the AlphaFold confidence is very low, and the Neural Net Objective is completely lukewarm.
Many sequences are not expected to fold at all, and in the real world these will adopt an "intrinsically disordered" or "random coil" structure. In such cases, we would expect AlphaFold to predict a relatively featureless distogram, where every residue-residue distance is represented as a flat distribution (i.e. "the distance between these two residues could be anything"). Probably the AlphaFold predicted structure will be very loopy and loosely-packed.
In this case, the distogram cross entropy will not be good, but also it may not be especially bad. We might interpret this like AlphaFold saying, "I don't see any evidence that your design will fold into this structure, but also I don't see any evidence that it will fold into anything else."
Yes, everything is exactly the same dark shade of grey. I'll share, next time I log into the game.
I think I may be experiencing a "1D10T" error. I really don't understand how to use this tool.
Okay, I upload my solution to AlphaFold and wait for it to spit out some percentages. What am I supposed to do, next? Can y'all please give us some training?
For the past two hours or so, I've attempted (unsuccessfully) to upload to AF. My [circa] midnight uploads transmitted and rendered results but since this morning, nada. Are any other players experiencing this problem?
AF worked perfectly in the past but since today I have the same problem. I guess the server is down/crashed.
Yes, it looks like the AlphaFold server is currently down for everyone. We're looking into the issue.
I have noticed in the last weeks that the amount of uploadable solutions to scientists is very limited. For this puzzle I can only upload 5 solutions. Is this intended? I would have more to share but I do get some message like "too many shared solutions..." I can upload many more to teammembers though. Is this a bug or a feature? I think this cropped up since AF was introduced but I am mot sure there.
Yes, we currently limit AlphaFold submissions to maximum 5 pending requests at any time. Once a pending job completes, then you may submit a new job.
Since our AlphaFold server is currently down, pending jobs are not completing. Once we get the server back online and your pending jobs are completed, then you will be able to make new submissions. Apologies for the unexpected downtime!
I did not mean uploads to alphafold but instead the upload of a solution to scientists in the filedialog (where I could also upload to group or to myself). THIS is limited to 5 for me in shares to scientists. Or are the number of pending uploads to AF and the number of shareable solutions in filedialog coupled? I would find that strange.
Anyway, thx for trying to get the AF server back online. I will have to stall my investigations until it is available. Good luck in getting it back up again!
Sorry, I misread your comment! Yes, players are limited to 5 shares with scientists in each puzzle; we will increase it to 10.
The purpose of the limit is to reduce spam, and discourage players from sharing with scientists every time they make a minor change to their solution.
The Share with Scientists limit is unrelated to the AlphaFold submission limit.
It would be great to be able to share a bit more to scientists - especially for these kind of puzzles which are designed to try a multitude of different approaches. Thx!
I noticed that the higher my foldit points, the higher the AF confidence.
It's disappointing because this doesn't help me to select early designs with higher confidence. On end play, the AF doesn't help to select and finish with high confidence solutions (because most of them are high, and if a high score isn't, I still shall end with this for pure competition).
I think that a small bonus related to confidence (once you stop mutating) could help to align high score with confidence.
Neural Net (max +0)
Achieve an AlphaFold prediction confidence of 80% or more.